Multiple sequence alignment - TraesCS4B01G111400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS4B01G111400 chr4B 100.000 6118 0 0 1 6118 124924233 124918116 0.000000e+00 11298.0
1 TraesCS4B01G111400 chr4B 82.011 189 30 4 1436 1623 417139916 417140101 2.280000e-34 158.0
2 TraesCS4B01G111400 chr4D 92.173 1942 73 24 4219 6118 88144733 88142829 0.000000e+00 2671.0
3 TraesCS4B01G111400 chr4D 89.871 1629 94 34 64 1650 88149581 88147982 0.000000e+00 2028.0
4 TraesCS4B01G111400 chr4D 96.827 977 23 5 2468 3443 88147823 88146854 0.000000e+00 1626.0
5 TraesCS4B01G111400 chr4D 95.778 379 15 1 3477 3854 88146853 88146475 1.460000e-170 610.0
6 TraesCS4B01G111400 chr4D 93.103 377 18 3 3852 4220 88146394 88146018 4.170000e-151 545.0
7 TraesCS4B01G111400 chr4D 90.833 120 10 1 2371 2489 88147982 88147863 6.350000e-35 159.0
8 TraesCS4B01G111400 chr4A 91.097 1741 77 38 4089 5788 501126938 501125235 0.000000e+00 2285.0
9 TraesCS4B01G111400 chr4A 95.533 1388 50 6 2468 3851 501128461 501127082 0.000000e+00 2209.0
10 TraesCS4B01G111400 chr4A 90.006 1681 96 32 1 1650 501130246 501128607 0.000000e+00 2108.0
11 TraesCS4B01G111400 chr4A 95.376 346 16 0 5773 6118 501125218 501124873 8.960000e-153 551.0
12 TraesCS4B01G111400 chr4A 82.007 289 48 4 2583 2868 7329972 7330259 6.130000e-60 243.0
13 TraesCS4B01G111400 chr4A 81.544 298 52 3 2583 2878 593661616 593661320 6.130000e-60 243.0
14 TraesCS4B01G111400 chr4A 77.244 312 55 9 4598 4908 501126260 501125964 1.050000e-37 169.0
15 TraesCS4B01G111400 chr4A 89.394 66 6 1 2370 2434 501128609 501128544 1.410000e-11 82.4
16 TraesCS4B01G111400 chrUn 99.722 719 2 0 1651 2369 77421386 77422104 0.000000e+00 1317.0
17 TraesCS4B01G111400 chrUn 99.722 719 2 0 1651 2369 352589276 352588558 0.000000e+00 1317.0
18 TraesCS4B01G111400 chrUn 86.408 103 12 2 1392 1493 81439853 81439752 1.800000e-20 111.0
19 TraesCS4B01G111400 chr6B 99.722 719 2 0 1651 2369 91149101 91148383 0.000000e+00 1317.0
20 TraesCS4B01G111400 chr6B 97.775 719 12 2 1651 2369 561264235 561263521 0.000000e+00 1236.0
21 TraesCS4B01G111400 chr6B 81.849 292 50 3 2583 2872 541150211 541150501 6.130000e-60 243.0
22 TraesCS4B01G111400 chr7A 98.630 730 7 2 1643 2369 201524344 201523615 0.000000e+00 1290.0
23 TraesCS4B01G111400 chr7A 85.492 193 25 3 1433 1624 664370858 664370668 1.350000e-46 198.0
24 TraesCS4B01G111400 chr7A 84.615 91 13 1 1381 1470 661295693 661295603 8.450000e-14 89.8
25 TraesCS4B01G111400 chr5A 98.192 719 11 1 1651 2369 595424238 595424954 0.000000e+00 1254.0
26 TraesCS4B01G111400 chr5A 81.544 298 52 3 2583 2878 309289077 309288781 6.130000e-60 243.0
27 TraesCS4B01G111400 chr5A 81.928 249 30 10 1381 1618 634499708 634499464 4.840000e-46 196.0
28 TraesCS4B01G111400 chr3B 98.192 719 11 1 1651 2369 148434362 148433646 0.000000e+00 1254.0
29 TraesCS4B01G111400 chr1B 97.636 719 15 1 1651 2369 91563363 91562647 0.000000e+00 1232.0
30 TraesCS4B01G111400 chr1B 81.208 298 53 3 2583 2878 179883118 179882822 2.850000e-58 237.0
31 TraesCS4B01G111400 chr1B 81.208 298 53 3 2583 2878 179885288 179884992 2.850000e-58 237.0
32 TraesCS4B01G111400 chr1B 86.592 179 19 5 1448 1623 288400949 288401125 6.260000e-45 193.0
33 TraesCS4B01G111400 chr1A 97.636 719 15 1 1651 2369 11309079 11308363 0.000000e+00 1232.0
34 TraesCS4B01G111400 chr7D 81.724 290 50 3 2585 2872 411546693 411546981 7.930000e-59 239.0
35 TraesCS4B01G111400 chr7D 81.379 290 36 11 3932 4203 62939580 62939291 2.870000e-53 220.0
36 TraesCS4B01G111400 chr7D 80.903 288 39 10 3932 4203 62193204 62192917 4.800000e-51 213.0
37 TraesCS4B01G111400 chr3D 81.949 277 37 7 3939 4207 326235103 326235374 7.980000e-54 222.0
38 TraesCS4B01G111400 chr2D 80.576 278 36 10 3941 4207 524330360 524330090 1.350000e-46 198.0
39 TraesCS4B01G111400 chr3A 80.074 271 37 9 3947 4207 438622014 438621751 1.050000e-42 185.0
40 TraesCS4B01G111400 chr6D 79.615 260 35 10 1380 1623 338738582 338738325 2.930000e-38 171.0
41 TraesCS4B01G111400 chr2B 85.526 152 22 0 1417 1568 47370371 47370220 6.350000e-35 159.0
42 TraesCS4B01G111400 chr5B 81.407 199 18 12 1433 1618 637447741 637447549 1.780000e-30 145.0
43 TraesCS4B01G111400 chr7B 83.908 87 14 0 1384 1470 629027617 629027531 3.930000e-12 84.2
44 TraesCS4B01G111400 chr2A 86.792 53 6 1 2427 2479 716916331 716916280 2.380000e-04 58.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS4B01G111400 chr4B 124918116 124924233 6117 True 11298.000000 11298 100.0000 1 6118 1 chr4B.!!$R1 6117
1 TraesCS4B01G111400 chr4D 88142829 88149581 6752 True 1273.166667 2671 93.0975 64 6118 6 chr4D.!!$R1 6054
2 TraesCS4B01G111400 chr4A 501124873 501130246 5373 True 1234.066667 2285 89.7750 1 6118 6 chr4A.!!$R2 6117
3 TraesCS4B01G111400 chrUn 77421386 77422104 718 False 1317.000000 1317 99.7220 1651 2369 1 chrUn.!!$F1 718
4 TraesCS4B01G111400 chrUn 352588558 352589276 718 True 1317.000000 1317 99.7220 1651 2369 1 chrUn.!!$R2 718
5 TraesCS4B01G111400 chr6B 91148383 91149101 718 True 1317.000000 1317 99.7220 1651 2369 1 chr6B.!!$R1 718
6 TraesCS4B01G111400 chr6B 561263521 561264235 714 True 1236.000000 1236 97.7750 1651 2369 1 chr6B.!!$R2 718
7 TraesCS4B01G111400 chr7A 201523615 201524344 729 True 1290.000000 1290 98.6300 1643 2369 1 chr7A.!!$R1 726
8 TraesCS4B01G111400 chr5A 595424238 595424954 716 False 1254.000000 1254 98.1920 1651 2369 1 chr5A.!!$F1 718
9 TraesCS4B01G111400 chr3B 148433646 148434362 716 True 1254.000000 1254 98.1920 1651 2369 1 chr3B.!!$R1 718
10 TraesCS4B01G111400 chr1B 91562647 91563363 716 True 1232.000000 1232 97.6360 1651 2369 1 chr1B.!!$R1 718
11 TraesCS4B01G111400 chr1B 179882822 179885288 2466 True 237.000000 237 81.2080 2583 2878 2 chr1B.!!$R2 295
12 TraesCS4B01G111400 chr1A 11308363 11309079 716 True 1232.000000 1232 97.6360 1651 2369 1 chr1A.!!$R1 718

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
470 486 0.103208 CCCCTGTCGATTCTTCTCCG 59.897 60.000 0.00 0.0 0.00 4.63 F
1377 1446 0.246635 AGGTATGTGTCCGTGCTGTC 59.753 55.000 0.00 0.0 0.00 3.51 F
2376 2459 0.172578 GAATGCCCAGCCGTTTTACC 59.827 55.000 0.00 0.0 0.00 2.85 F
2378 2461 0.324275 ATGCCCAGCCGTTTTACCAT 60.324 50.000 0.00 0.0 0.00 3.55 F
2621 2764 1.269102 CCTGTTCGAGTCTGACAACGT 60.269 52.381 20.18 0.0 0.00 3.99 F
4011 6538 1.302431 TGTGCTTCCACACCATCCG 60.302 57.895 0.00 0.0 46.51 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1387 1456 1.489230 AGAAATACTTAGCCCCCGTGG 59.511 52.381 0.00 0.00 37.09 4.94 R
3365 5687 0.678048 AATGAGCGAAAGGACAGGGC 60.678 55.000 0.00 0.00 0.00 5.19 R
3739 6061 0.232303 GTTGTGTGCTCGGAAAGACG 59.768 55.000 0.00 0.00 0.00 4.18 R
3885 6409 2.418628 ACAAACCAGTCACGTGTGAAAG 59.581 45.455 16.51 4.72 41.85 2.62 R
4449 8267 1.134280 CCCTCTGCCTCTACCATTGTG 60.134 57.143 0.00 0.00 0.00 3.33 R
5636 9495 0.099436 GCTTAGTTTGCGATGGCTGG 59.901 55.000 0.15 0.00 40.82 4.85 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.931281 TGGCACTCTAGATGTAAATATTGCTC 59.069 38.462 0.00 0.00 0.00 4.26
28 29 8.087750 GCACTCTAGATGTAAATATTGCTCTCT 58.912 37.037 0.00 0.00 0.00 3.10
35 40 9.035607 AGATGTAAATATTGCTCTCTACAAACG 57.964 33.333 0.00 0.00 0.00 3.60
55 60 7.330700 ACAAACGTGATCAATTTGTGAAGTTTT 59.669 29.630 26.80 9.51 43.19 2.43
56 61 7.826260 AACGTGATCAATTTGTGAAGTTTTT 57.174 28.000 0.00 0.00 40.50 1.94
80 85 5.446143 TTTTGAAAATCTACATGCACCGT 57.554 34.783 0.00 0.00 0.00 4.83
140 145 2.592993 GGCAGGCCCTGTAGTGACA 61.593 63.158 13.35 0.00 33.43 3.58
170 175 3.414700 CGCAGTCCCACTTGTCGC 61.415 66.667 0.00 0.00 0.00 5.19
265 270 2.419895 CGCGCGAACGAACGTCTAA 61.420 57.895 28.94 0.00 43.93 2.10
303 308 0.457035 GTAGGGACGACCGTAATGCA 59.543 55.000 7.88 0.00 46.96 3.96
350 355 3.135716 TTCCCCAGTTCCCCCTCCA 62.136 63.158 0.00 0.00 0.00 3.86
351 356 3.339093 CCCCAGTTCCCCCTCCAC 61.339 72.222 0.00 0.00 0.00 4.02
352 357 3.339093 CCCAGTTCCCCCTCCACC 61.339 72.222 0.00 0.00 0.00 4.61
353 358 3.339093 CCAGTTCCCCCTCCACCC 61.339 72.222 0.00 0.00 0.00 4.61
354 359 3.339093 CAGTTCCCCCTCCACCCC 61.339 72.222 0.00 0.00 0.00 4.95
387 393 1.304952 CCCTCCTCACTCTCTCCGT 59.695 63.158 0.00 0.00 0.00 4.69
440 456 0.338467 TCGATTCCTTCCCCCTCTCA 59.662 55.000 0.00 0.00 0.00 3.27
441 457 1.062121 TCGATTCCTTCCCCCTCTCAT 60.062 52.381 0.00 0.00 0.00 2.90
442 458 1.346068 CGATTCCTTCCCCCTCTCATC 59.654 57.143 0.00 0.00 0.00 2.92
443 459 1.702401 GATTCCTTCCCCCTCTCATCC 59.298 57.143 0.00 0.00 0.00 3.51
444 460 0.725133 TTCCTTCCCCCTCTCATCCT 59.275 55.000 0.00 0.00 0.00 3.24
445 461 0.266152 TCCTTCCCCCTCTCATCCTC 59.734 60.000 0.00 0.00 0.00 3.71
450 466 2.206536 CCCCTCTCATCCTCCTCGC 61.207 68.421 0.00 0.00 0.00 5.03
455 471 3.765257 CTCATCCTCCTCGCCCCCT 62.765 68.421 0.00 0.00 0.00 4.79
467 483 1.908483 GCCCCCTGTCGATTCTTCT 59.092 57.895 0.00 0.00 0.00 2.85
468 484 0.179070 GCCCCCTGTCGATTCTTCTC 60.179 60.000 0.00 0.00 0.00 2.87
469 485 0.466124 CCCCCTGTCGATTCTTCTCC 59.534 60.000 0.00 0.00 0.00 3.71
470 486 0.103208 CCCCTGTCGATTCTTCTCCG 59.897 60.000 0.00 0.00 0.00 4.63
471 487 1.103803 CCCTGTCGATTCTTCTCCGA 58.896 55.000 0.00 0.00 0.00 4.55
472 488 1.683917 CCCTGTCGATTCTTCTCCGAT 59.316 52.381 0.00 0.00 34.71 4.18
474 490 3.376540 CCTGTCGATTCTTCTCCGATTC 58.623 50.000 0.00 0.00 34.71 2.52
475 491 3.039405 CTGTCGATTCTTCTCCGATTCG 58.961 50.000 0.00 0.00 37.84 3.34
507 533 2.034607 GCTAGGAGCCGATTCGACT 58.965 57.895 7.83 0.00 34.48 4.18
580 607 3.864686 CCCTGTTCGCGCCATTCG 61.865 66.667 0.00 0.00 42.12 3.34
675 702 2.928334 CTGGATCAGGAATTCAGGGTG 58.072 52.381 7.93 0.00 37.34 4.61
706 733 2.748058 TTTGCTCCTTCGTGCTCCCC 62.748 60.000 0.00 0.00 0.00 4.81
758 785 2.046023 CATGGCGTGCCTTCCTCA 60.046 61.111 12.84 0.00 36.94 3.86
846 873 1.543134 GGGTAGGGTTCTTGGGGGT 60.543 63.158 0.00 0.00 0.00 4.95
907 938 4.267214 GTCGCCTCTTACGTTTTTATCCTC 59.733 45.833 0.00 0.00 0.00 3.71
979 1015 0.381089 GCTGCTCTTGCCATGCTAAG 59.619 55.000 0.00 0.00 38.71 2.18
1128 1164 1.511850 TGTCGTTGCTTGAGGTGATG 58.488 50.000 0.00 0.00 0.00 3.07
1144 1180 0.957362 GATGCCCCTTGCTATGCTTC 59.043 55.000 0.00 0.00 42.00 3.86
1208 1272 8.761575 ACAATTTCTTTGTATGCCATGTTTAG 57.238 30.769 0.00 0.00 46.75 1.85
1273 1337 1.561076 TGCTCAACATCCTATGCCTGT 59.439 47.619 0.00 0.00 0.00 4.00
1374 1443 1.848652 ACTAGGTATGTGTCCGTGCT 58.151 50.000 0.00 0.00 0.00 4.40
1377 1446 0.246635 AGGTATGTGTCCGTGCTGTC 59.753 55.000 0.00 0.00 0.00 3.51
1379 1448 1.076533 GTATGTGTCCGTGCTGTCCG 61.077 60.000 0.00 0.00 0.00 4.79
1380 1449 1.529152 TATGTGTCCGTGCTGTCCGT 61.529 55.000 0.00 0.00 0.00 4.69
1381 1450 3.036084 GTGTCCGTGCTGTCCGTG 61.036 66.667 0.00 0.00 0.00 4.94
1382 1451 4.961511 TGTCCGTGCTGTCCGTGC 62.962 66.667 0.00 0.00 0.00 5.34
1386 1455 4.354212 CGTGCTGTCCGTGCGTTG 62.354 66.667 0.00 0.00 0.00 4.10
1387 1456 4.666532 GTGCTGTCCGTGCGTTGC 62.667 66.667 0.00 0.00 0.00 4.17
1390 1459 4.012895 CTGTCCGTGCGTTGCCAC 62.013 66.667 0.00 0.00 0.00 5.01
1406 1475 1.963172 CCACGGGGGCTAAGTATTTC 58.037 55.000 0.00 0.00 0.00 2.17
1553 1622 6.016024 TGTGCCCATGATTAATCTGCTTTATC 60.016 38.462 16.24 2.82 0.00 1.75
1602 1673 7.836685 TGGTTGATATTTATTTACTTCTGGGCA 59.163 33.333 0.00 0.00 0.00 5.36
2369 2452 1.101049 ATAAACCGAATGCCCAGCCG 61.101 55.000 0.00 0.00 0.00 5.52
2370 2453 2.472414 TAAACCGAATGCCCAGCCGT 62.472 55.000 0.00 0.00 0.00 5.68
2371 2454 3.860930 AACCGAATGCCCAGCCGTT 62.861 57.895 0.00 0.00 0.00 4.44
2372 2455 3.061848 CCGAATGCCCAGCCGTTT 61.062 61.111 0.00 0.00 0.00 3.60
2373 2456 2.635443 CCGAATGCCCAGCCGTTTT 61.635 57.895 0.00 0.00 0.00 2.43
2374 2457 1.309499 CCGAATGCCCAGCCGTTTTA 61.309 55.000 0.00 0.00 0.00 1.52
2375 2458 0.179174 CGAATGCCCAGCCGTTTTAC 60.179 55.000 0.00 0.00 0.00 2.01
2376 2459 0.172578 GAATGCCCAGCCGTTTTACC 59.827 55.000 0.00 0.00 0.00 2.85
2377 2460 0.540830 AATGCCCAGCCGTTTTACCA 60.541 50.000 0.00 0.00 0.00 3.25
2378 2461 0.324275 ATGCCCAGCCGTTTTACCAT 60.324 50.000 0.00 0.00 0.00 3.55
2418 2501 7.745620 ATGGACCGTGGATTTATTTCTAATC 57.254 36.000 0.00 0.00 0.00 1.75
2423 2506 6.828785 ACCGTGGATTTATTTCTAATCTGCTT 59.171 34.615 0.00 0.00 33.51 3.91
2496 2639 4.901250 ACAAAACTGGGTGAAAGATGGAAT 59.099 37.500 0.00 0.00 0.00 3.01
2497 2640 5.221501 ACAAAACTGGGTGAAAGATGGAATG 60.222 40.000 0.00 0.00 0.00 2.67
2498 2641 2.450476 ACTGGGTGAAAGATGGAATGC 58.550 47.619 0.00 0.00 0.00 3.56
2509 2652 6.375455 TGAAAGATGGAATGCTAGGTTCTTTC 59.625 38.462 13.01 13.01 43.74 2.62
2516 2659 8.090788 TGGAATGCTAGGTTCTTTCTAAGTAT 57.909 34.615 0.00 0.00 0.00 2.12
2588 2731 8.718102 TTGGTTAATATTCTGTAGTGCTTCTC 57.282 34.615 0.00 0.00 0.00 2.87
2610 2753 4.082190 TCTGTCCATTACTTCCTGTTCGAG 60.082 45.833 0.00 0.00 0.00 4.04
2611 2754 3.576982 TGTCCATTACTTCCTGTTCGAGT 59.423 43.478 0.00 0.00 0.00 4.18
2621 2764 1.269102 CCTGTTCGAGTCTGACAACGT 60.269 52.381 20.18 0.00 0.00 3.99
2677 4991 8.718734 GTTTCACTTACTTACCATTCGATCTTT 58.281 33.333 0.00 0.00 0.00 2.52
2718 5034 9.734620 TGCATGTTATCAGCTTAATAAAATGAC 57.265 29.630 22.23 16.44 36.82 3.06
2808 5125 9.533253 CAGTCATTATTTTCTGAAAACCTGTTT 57.467 29.630 17.06 4.00 32.37 2.83
2854 5171 8.713708 TTTTTCAGAATCCCTAAATGGTGTTA 57.286 30.769 0.00 0.00 0.00 2.41
2855 5172 8.893563 TTTTCAGAATCCCTAAATGGTGTTAT 57.106 30.769 0.00 0.00 0.00 1.89
2856 5173 8.893563 TTTCAGAATCCCTAAATGGTGTTATT 57.106 30.769 0.00 0.00 0.00 1.40
2985 5307 1.559682 ACTATCAAAGCCATGGGACGT 59.440 47.619 15.13 0.00 0.00 4.34
3365 5687 1.839994 TCATCTCCAGGGTAAGGCAAG 59.160 52.381 0.00 0.00 0.00 4.01
3472 5794 5.304101 TGTTGTTCAATATTGGAAACTGGCT 59.696 36.000 15.36 0.00 0.00 4.75
3563 5885 6.922957 TGAAACCTGCTTTTGATTATGAACAC 59.077 34.615 0.00 0.00 0.00 3.32
3597 5919 2.227089 GAGTTGATCCGCTCCACCGT 62.227 60.000 3.10 0.00 0.00 4.83
3676 5998 1.674057 CTTTCCCTCTGCTCGTGGT 59.326 57.895 0.00 0.00 0.00 4.16
3727 6049 2.386935 GGGCAGGGGCAGAGGTATT 61.387 63.158 0.00 0.00 43.71 1.89
3766 6088 2.146342 CCGAGCACACAACTTTCAGAT 58.854 47.619 0.00 0.00 0.00 2.90
3784 6106 4.777896 TCAGATAGTAACTCATATGGCCCC 59.222 45.833 0.00 0.00 0.00 5.80
3817 6139 8.636843 CGACCGTATCTTTATAACTTTAGCATC 58.363 37.037 0.00 0.00 0.00 3.91
3836 6158 2.950781 TCCCATGTTGCCAAGTTACAA 58.049 42.857 0.00 0.00 0.00 2.41
3885 6409 4.622457 GCTTACTCCTTTACACCCTGTACC 60.622 50.000 0.00 0.00 31.69 3.34
3893 6417 2.632987 ACACCCTGTACCTTTCACAC 57.367 50.000 0.00 0.00 0.00 3.82
3923 6447 6.909076 TGGTTTGTTTACCTACCTTCCTAAA 58.091 36.000 0.00 0.00 39.04 1.85
3931 6455 5.899631 ACCTACCTTCCTAAAAACTGACA 57.100 39.130 0.00 0.00 0.00 3.58
3970 6497 3.312736 AGACAAACCCCACAAGTCATT 57.687 42.857 0.00 0.00 0.00 2.57
4011 6538 1.302431 TGTGCTTCCACACCATCCG 60.302 57.895 0.00 0.00 46.51 4.18
4080 6611 3.754850 TCCGATTTGAACGAGTCACTCTA 59.245 43.478 2.61 0.00 35.39 2.43
4114 6645 6.482898 TGCATAGTGGATTTTAAATGCCAT 57.517 33.333 11.37 0.00 39.11 4.40
4134 6665 7.834803 TGCCATCACATTTAATTTATGACACA 58.165 30.769 7.11 0.00 0.00 3.72
4259 8077 2.309613 TCACAGTGCTTCAATTGGCTT 58.690 42.857 5.42 0.00 0.00 4.35
4320 8138 2.698803 TGTTCAGAGTGCATGCGTTAT 58.301 42.857 14.09 0.00 0.00 1.89
4327 8145 5.641636 TCAGAGTGCATGCGTTATTTTCTTA 59.358 36.000 14.09 0.00 0.00 2.10
4449 8267 4.090819 GGAGGAGGATGGAGACTATTACC 58.909 52.174 0.00 0.00 0.00 2.85
4601 8419 1.476833 CGGGGTGGATACTTTGATGGG 60.477 57.143 0.00 0.00 37.61 4.00
4647 8465 0.613853 AGGCCGTGGTAAGCTCAGTA 60.614 55.000 0.00 0.00 0.00 2.74
4754 8573 2.025887 GGGGAAGAAGAATGGAGCAGAA 60.026 50.000 0.00 0.00 0.00 3.02
4819 8638 1.226323 CGTGGTAAGCTCGGTCTCG 60.226 63.158 0.00 0.00 37.82 4.04
4931 8750 5.282055 TGGAGCAGAATGAATACTTCGAT 57.718 39.130 0.00 0.00 39.69 3.59
4932 8751 5.052481 TGGAGCAGAATGAATACTTCGATG 58.948 41.667 0.00 0.00 39.69 3.84
4933 8752 4.450419 GGAGCAGAATGAATACTTCGATGG 59.550 45.833 3.12 0.00 39.69 3.51
4934 8753 5.282055 AGCAGAATGAATACTTCGATGGA 57.718 39.130 3.12 0.00 39.69 3.41
4994 8813 5.221322 GCTCTGGTGTGACATATCATAGTGA 60.221 44.000 0.00 0.00 37.14 3.41
5187 9032 0.394938 TACGGTGTTGCTCCATGTGT 59.605 50.000 0.00 0.00 0.00 3.72
5188 9033 0.465460 ACGGTGTTGCTCCATGTGTT 60.465 50.000 0.00 0.00 0.00 3.32
5215 9060 4.433615 TCTCTGACGTGAATCTTTATGGC 58.566 43.478 0.00 0.00 0.00 4.40
5216 9061 4.160439 TCTCTGACGTGAATCTTTATGGCT 59.840 41.667 0.00 0.00 0.00 4.75
5217 9062 4.832248 TCTGACGTGAATCTTTATGGCTT 58.168 39.130 0.00 0.00 0.00 4.35
5218 9063 5.245531 TCTGACGTGAATCTTTATGGCTTT 58.754 37.500 0.00 0.00 0.00 3.51
5219 9064 6.403049 TCTGACGTGAATCTTTATGGCTTTA 58.597 36.000 0.00 0.00 0.00 1.85
5220 9065 7.047891 TCTGACGTGAATCTTTATGGCTTTAT 58.952 34.615 0.00 0.00 0.00 1.40
5221 9066 7.011389 TCTGACGTGAATCTTTATGGCTTTATG 59.989 37.037 0.00 0.00 0.00 1.90
5222 9067 6.038161 TGACGTGAATCTTTATGGCTTTATGG 59.962 38.462 0.00 0.00 0.00 2.74
5310 9155 1.021390 CCAGCCAGCAAAGTACCTCG 61.021 60.000 0.00 0.00 0.00 4.63
5425 9276 0.924090 GCTTCGAAGTCTGCCGTATG 59.076 55.000 25.24 0.00 0.00 2.39
5426 9277 0.924090 CTTCGAAGTCTGCCGTATGC 59.076 55.000 17.24 0.00 41.77 3.14
5427 9278 0.459585 TTCGAAGTCTGCCGTATGCC 60.460 55.000 0.00 0.00 40.16 4.40
5428 9279 1.141881 CGAAGTCTGCCGTATGCCT 59.858 57.895 0.00 0.00 40.16 4.75
5429 9280 1.148157 CGAAGTCTGCCGTATGCCTG 61.148 60.000 0.00 0.00 40.16 4.85
5510 9361 0.251564 AATGCGGGGGATCACACAAA 60.252 50.000 0.00 0.00 0.00 2.83
5511 9362 0.965363 ATGCGGGGGATCACACAAAC 60.965 55.000 0.00 0.00 0.00 2.93
5513 9364 1.175983 GCGGGGGATCACACAAACAA 61.176 55.000 0.00 0.00 0.00 2.83
5514 9365 1.544724 CGGGGGATCACACAAACAAT 58.455 50.000 0.00 0.00 0.00 2.71
5515 9366 2.717390 CGGGGGATCACACAAACAATA 58.283 47.619 0.00 0.00 0.00 1.90
5516 9367 2.682856 CGGGGGATCACACAAACAATAG 59.317 50.000 0.00 0.00 0.00 1.73
5570 9429 1.970917 GCCGCTCTCCGTGTGAATTG 61.971 60.000 0.00 0.00 34.38 2.32
5571 9430 1.421485 CGCTCTCCGTGTGAATTGC 59.579 57.895 0.00 0.00 0.00 3.56
5593 9452 5.992829 TGCGTCCTGATTTCTTACAAAGTTA 59.007 36.000 0.00 0.00 0.00 2.24
5596 9455 7.095355 GCGTCCTGATTTCTTACAAAGTTAAGA 60.095 37.037 0.00 0.00 0.00 2.10
5626 9485 7.596494 AGAAGTACAGTGTACGTAGCAAATAA 58.404 34.615 24.13 0.00 0.00 1.40
5629 9488 7.373493 AGTACAGTGTACGTAGCAAATAAGTT 58.627 34.615 24.13 2.53 0.00 2.66
5636 9495 8.108782 GTGTACGTAGCAAATAAGTTCAGATTC 58.891 37.037 0.00 0.00 0.00 2.52
5660 9519 2.855180 CCATCGCAAACTAAGCACAAG 58.145 47.619 0.00 0.00 0.00 3.16
5692 9551 0.812014 TGCGGTTGAAACTGAAGCGA 60.812 50.000 6.19 0.00 44.91 4.93
5738 9597 9.579768 GTATACTGTGACATCATATCAGATTCC 57.420 37.037 5.30 0.00 0.00 3.01
5743 9602 6.558394 TGTGACATCATATCAGATTCCCCTTA 59.442 38.462 0.00 0.00 0.00 2.69
5823 9731 2.426738 CTGCAGAAGAGAACGAGGAGAT 59.573 50.000 8.42 0.00 0.00 2.75
5827 9735 3.194542 CAGAAGAGAACGAGGAGATTGGT 59.805 47.826 0.00 0.00 0.00 3.67
5861 9769 2.959421 AGTCTTCCTCCCAGGAGAAT 57.041 50.000 15.53 0.00 46.73 2.40
5965 9879 0.410663 TCTTCCTCCCCACTTCCGTA 59.589 55.000 0.00 0.00 0.00 4.02
5992 9906 3.145551 CCCTGCAGCCATGGAAGC 61.146 66.667 18.40 18.63 0.00 3.86
5993 9907 2.044252 CCTGCAGCCATGGAAGCT 60.044 61.111 18.40 1.76 42.70 3.74
6057 9971 1.003051 TCCTTACCCTGCCTCCTCC 59.997 63.158 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.786401 AATTGATCACGTTTGTAGAGAGC 57.214 39.130 0.00 0.00 0.00 4.09
23 24 7.011773 CACAAATTGATCACGTTTGTAGAGAG 58.988 38.462 25.96 15.90 42.35 3.20
25 26 6.887368 TCACAAATTGATCACGTTTGTAGAG 58.113 36.000 25.96 18.50 42.35 2.43
28 29 7.022055 ACTTCACAAATTGATCACGTTTGTA 57.978 32.000 25.96 16.68 42.35 2.41
57 62 5.837437 ACGGTGCATGTAGATTTTCAAAAA 58.163 33.333 0.00 0.00 0.00 1.94
60 65 5.009110 TCAAACGGTGCATGTAGATTTTCAA 59.991 36.000 0.00 0.00 0.00 2.69
61 66 4.517075 TCAAACGGTGCATGTAGATTTTCA 59.483 37.500 0.00 0.00 0.00 2.69
62 67 5.041951 TCAAACGGTGCATGTAGATTTTC 57.958 39.130 0.00 0.00 0.00 2.29
71 76 0.606401 ACTCCCTCAAACGGTGCATG 60.606 55.000 0.00 0.00 0.00 4.06
80 85 5.163447 CCTGTGATAACGATACTCCCTCAAA 60.163 44.000 0.00 0.00 0.00 2.69
120 125 0.976073 GTCACTACAGGGCCTGCCTA 60.976 60.000 33.04 17.74 34.37 3.93
170 175 0.604780 CACTGTCAGTTGAGGCCAGG 60.605 60.000 5.01 0.00 0.00 4.45
250 255 0.246260 CGCTTTAGACGTTCGTTCGC 60.246 55.000 0.00 0.00 0.00 4.70
265 270 4.681978 GGTGACGTGGAGGCGCTT 62.682 66.667 7.64 0.00 38.75 4.68
303 308 1.745115 CGTGTGCGGGTTCATGGAT 60.745 57.895 0.00 0.00 0.00 3.41
350 355 4.025858 TCTCGAGGTCGACGGGGT 62.026 66.667 13.56 0.00 44.22 4.95
351 356 3.507009 GTCTCGAGGTCGACGGGG 61.507 72.222 13.56 1.20 44.22 5.73
352 357 3.507009 GGTCTCGAGGTCGACGGG 61.507 72.222 13.56 0.00 44.22 5.28
353 358 3.507009 GGGTCTCGAGGTCGACGG 61.507 72.222 13.56 1.31 44.22 4.79
354 359 3.507009 GGGGTCTCGAGGTCGACG 61.507 72.222 13.56 0.00 44.22 5.12
387 393 3.842923 GCTGCTCCGCTCTGCCTA 61.843 66.667 0.00 0.00 0.00 3.93
440 456 4.095400 ACAGGGGGCGAGGAGGAT 62.095 66.667 0.00 0.00 0.00 3.24
441 457 4.779733 GACAGGGGGCGAGGAGGA 62.780 72.222 0.00 0.00 0.00 3.71
444 460 3.976490 AATCGACAGGGGGCGAGGA 62.976 63.158 0.00 0.00 40.14 3.71
445 461 3.447025 GAATCGACAGGGGGCGAGG 62.447 68.421 0.00 0.00 40.14 4.63
450 466 0.466124 GGAGAAGAATCGACAGGGGG 59.534 60.000 0.00 0.00 0.00 5.40
455 471 3.066369 CGAATCGGAGAAGAATCGACA 57.934 47.619 0.00 0.00 43.58 4.35
580 607 3.228688 GATTTCGCTCCGCATCGCC 62.229 63.158 0.00 0.00 0.00 5.54
615 642 2.034066 CCAAGGAAGCTGCCGGAA 59.966 61.111 5.05 0.00 0.00 4.30
706 733 4.156739 CGAATTTCTTGGAAAGGAAGAGGG 59.843 45.833 0.00 0.00 46.40 4.30
719 746 0.729140 GGCACGGTGCGAATTTCTTG 60.729 55.000 25.24 0.00 46.21 3.02
758 785 1.079503 GCGAAACGGAATGAGAAGCT 58.920 50.000 0.00 0.00 0.00 3.74
830 857 0.611062 GCAACCCCCAAGAACCCTAC 60.611 60.000 0.00 0.00 0.00 3.18
846 873 2.405805 CCGGCCACGATTCATGCAA 61.406 57.895 2.24 0.00 44.60 4.08
907 938 1.857217 CATGAAAGGAGATGAGACGCG 59.143 52.381 3.53 3.53 0.00 6.01
979 1015 5.347342 CATGGCTATGAATCGAGATAGGTC 58.653 45.833 3.54 0.00 36.36 3.85
1056 1092 0.938637 GCGCAGTGATCCTGATCTCG 60.939 60.000 0.30 8.98 44.49 4.04
1128 1164 1.440145 GACGAAGCATAGCAAGGGGC 61.440 60.000 0.00 0.00 45.30 5.80
1144 1180 2.969443 AAGGACAAAGCGAAATGACG 57.031 45.000 0.00 0.00 0.00 4.35
1200 1237 4.807304 GCATTTCCCAGATTGCTAAACATG 59.193 41.667 0.00 0.00 32.41 3.21
1203 1240 3.448660 AGGCATTTCCCAGATTGCTAAAC 59.551 43.478 0.00 0.00 35.46 2.01
1208 1272 0.383231 CGAGGCATTTCCCAGATTGC 59.617 55.000 0.00 0.00 34.51 3.56
1300 1364 2.156098 TCGGTGGCAAATAGAAACACC 58.844 47.619 0.00 0.00 46.14 4.16
1351 1420 3.879295 GCACGGACACATACCTAGTACTA 59.121 47.826 1.89 1.89 0.00 1.82
1352 1421 2.686915 GCACGGACACATACCTAGTACT 59.313 50.000 0.00 0.00 0.00 2.73
1353 1422 2.686915 AGCACGGACACATACCTAGTAC 59.313 50.000 0.00 0.00 0.00 2.73
1387 1456 1.489230 AGAAATACTTAGCCCCCGTGG 59.511 52.381 0.00 0.00 37.09 4.94
1388 1457 3.277142 AAGAAATACTTAGCCCCCGTG 57.723 47.619 0.00 0.00 37.03 4.94
1389 1458 4.225717 TGTTAAGAAATACTTAGCCCCCGT 59.774 41.667 0.00 0.00 41.33 5.28
1390 1459 4.573607 GTGTTAAGAAATACTTAGCCCCCG 59.426 45.833 0.00 0.00 41.33 5.73
1400 1469 9.871238 TGATCCTCTTACTGTGTTAAGAAATAC 57.129 33.333 0.00 0.00 32.61 1.89
1406 1475 7.875041 CCCATATGATCCTCTTACTGTGTTAAG 59.125 40.741 3.65 0.00 0.00 1.85
1553 1622 6.093082 CCAAACTCTTAGTATTTGGTAACCCG 59.907 42.308 16.35 0.00 44.87 5.28
1578 1649 8.903820 ACTGCCCAGAAGTAAATAAATATCAAC 58.096 33.333 1.69 0.00 0.00 3.18
2378 2461 9.640963 CCACGGTCCATAAATAAATTGTTTTTA 57.359 29.630 0.00 0.00 0.00 1.52
2418 2501 7.798596 AACCAGATCAATCTATGTAAAGCAG 57.201 36.000 0.00 0.00 34.85 4.24
2423 2506 9.573166 CCCAATAAACCAGATCAATCTATGTAA 57.427 33.333 0.00 0.00 34.85 2.41
2525 2668 5.254115 GGGCAGGTGTCTCTACTTTATTTT 58.746 41.667 0.00 0.00 0.00 1.82
2588 2731 4.177026 CTCGAACAGGAAGTAATGGACAG 58.823 47.826 0.00 0.00 0.00 3.51
2610 2753 5.459110 TTCACAAAGTTACGTTGTCAGAC 57.541 39.130 13.26 0.00 37.09 3.51
2611 2754 4.033587 GCTTCACAAAGTTACGTTGTCAGA 59.966 41.667 13.26 6.86 37.09 3.27
2621 2764 6.071616 ACAAACTGAAAGGCTTCACAAAGTTA 60.072 34.615 0.00 0.00 39.30 2.24
2677 4991 4.155063 ACATGCACATACTTCAGGCATA 57.845 40.909 0.00 0.00 42.81 3.14
2718 5034 3.696281 TGAACTGCACACAAGTTCATG 57.304 42.857 12.86 0.00 44.47 3.07
2808 5125 1.199615 TCTGTTGACCACTGACCACA 58.800 50.000 0.00 0.00 0.00 4.17
2985 5307 4.133820 CCATGACCGTCTTATTTATGGCA 58.866 43.478 0.00 0.00 0.00 4.92
3344 5666 2.196742 TGCCTTACCCTGGAGATGAT 57.803 50.000 0.00 0.00 0.00 2.45
3365 5687 0.678048 AATGAGCGAAAGGACAGGGC 60.678 55.000 0.00 0.00 0.00 5.19
3472 5794 4.155099 CCCACAATACGCAGACAAATTACA 59.845 41.667 0.00 0.00 0.00 2.41
3563 5885 1.528586 CAACTCAGAGCAACACCTTCG 59.471 52.381 0.00 0.00 0.00 3.79
3734 6056 1.009389 GTGCTCGGAAAGACGTGAGG 61.009 60.000 0.00 0.00 34.94 3.86
3739 6061 0.232303 GTTGTGTGCTCGGAAAGACG 59.768 55.000 0.00 0.00 0.00 4.18
3747 6069 3.990469 ACTATCTGAAAGTTGTGTGCTCG 59.010 43.478 0.00 0.00 33.76 5.03
3766 6088 3.116512 TCTGGGGGCCATATGAGTTACTA 60.117 47.826 4.39 0.00 30.82 1.82
3784 6106 2.649331 AAAGATACGGTCGTGTCTGG 57.351 50.000 20.11 0.00 43.98 3.86
3863 6387 4.776308 AGGTACAGGGTGTAAAGGAGTAAG 59.224 45.833 0.00 0.00 34.21 2.34
3885 6409 2.418628 ACAAACCAGTCACGTGTGAAAG 59.581 45.455 16.51 4.72 41.85 2.62
3893 6417 3.495753 GGTAGGTAAACAAACCAGTCACG 59.504 47.826 0.00 0.00 42.40 4.35
3970 6497 7.328982 CACACATGCACAGAAAAATAGCAATTA 59.671 33.333 0.00 0.00 38.85 1.40
3999 6526 5.298276 GCTATAAAAATTCGGATGGTGTGGA 59.702 40.000 0.00 0.00 0.00 4.02
4011 6538 8.667076 AGCAAATCCAATGGCTATAAAAATTC 57.333 30.769 0.00 0.00 34.25 2.17
4114 6645 9.891828 GTTGAGTGTGTCATAAATTAAATGTGA 57.108 29.630 1.79 0.00 34.17 3.58
4259 8077 9.354673 AGACTGAAAAATAAGTCCAGAAAATGA 57.645 29.630 0.00 0.00 43.18 2.57
4303 8121 4.002982 AGAAAATAACGCATGCACTCTGA 58.997 39.130 19.57 0.00 0.00 3.27
4310 8128 6.683090 TTGTTGTAAGAAAATAACGCATGC 57.317 33.333 7.91 7.91 0.00 4.06
4327 8145 8.181904 AGTTTCTTGTCCATATGATTTGTTGT 57.818 30.769 3.65 0.00 0.00 3.32
4376 8194 4.511826 GGTCCATTGCTAATAGCTGTACAC 59.488 45.833 13.88 5.01 42.97 2.90
4449 8267 1.134280 CCCTCTGCCTCTACCATTGTG 60.134 57.143 0.00 0.00 0.00 3.33
4601 8419 3.433740 GGGGTTGATACTCATCTGGTTCC 60.434 52.174 0.00 0.00 31.93 3.62
4754 8573 4.776349 TGGTTCGCCATTGTAGTATTCAT 58.224 39.130 0.00 0.00 43.56 2.57
4819 8638 2.648059 AGCCACAGAAAGATGGTATGC 58.352 47.619 0.00 0.00 38.34 3.14
4931 8750 3.720002 GGGGGTATTCATAAGGTTCTCCA 59.280 47.826 0.00 0.00 35.89 3.86
4932 8751 4.368565 GGGGGTATTCATAAGGTTCTCC 57.631 50.000 0.00 0.00 0.00 3.71
5111 8930 0.734889 GGCATGTCCCAGTTCAATCG 59.265 55.000 0.00 0.00 0.00 3.34
5158 9001 2.425668 AGCAACACCGTAAGCAAAAACT 59.574 40.909 0.00 0.00 0.00 2.66
5187 9032 0.976641 ATTCACGTCAGAGAGCCCAA 59.023 50.000 0.00 0.00 0.00 4.12
5188 9033 0.532573 GATTCACGTCAGAGAGCCCA 59.467 55.000 0.00 0.00 0.00 5.36
5215 9060 2.928334 ACAGCATCAGAGGCCATAAAG 58.072 47.619 5.01 0.00 0.00 1.85
5216 9061 3.741075 CGTACAGCATCAGAGGCCATAAA 60.741 47.826 5.01 0.00 0.00 1.40
5217 9062 2.224042 CGTACAGCATCAGAGGCCATAA 60.224 50.000 5.01 0.00 0.00 1.90
5218 9063 1.341209 CGTACAGCATCAGAGGCCATA 59.659 52.381 5.01 0.00 0.00 2.74
5219 9064 0.105593 CGTACAGCATCAGAGGCCAT 59.894 55.000 5.01 0.00 0.00 4.40
5220 9065 0.970427 TCGTACAGCATCAGAGGCCA 60.970 55.000 5.01 0.00 0.00 5.36
5221 9066 0.528684 GTCGTACAGCATCAGAGGCC 60.529 60.000 2.72 0.00 0.00 5.19
5222 9067 0.457851 AGTCGTACAGCATCAGAGGC 59.542 55.000 0.00 0.00 0.00 4.70
5310 9155 4.494350 TTCACACGTTCTACTAGGTGTC 57.506 45.455 0.00 0.00 43.13 3.67
5366 9217 4.808414 TTCACATCCACAGAGAGGTAAG 57.192 45.455 0.00 0.00 0.00 2.34
5400 9251 1.334149 GGCAGACTTCGAAGCAAACAC 60.334 52.381 24.86 9.64 0.00 3.32
5510 9361 4.707448 AGGTTCACGAGATGAGACTATTGT 59.293 41.667 0.00 0.00 38.99 2.71
5511 9362 5.039984 CAGGTTCACGAGATGAGACTATTG 58.960 45.833 0.00 0.00 38.99 1.90
5513 9364 4.274147 ACAGGTTCACGAGATGAGACTAT 58.726 43.478 0.00 0.00 38.99 2.12
5514 9365 3.687125 ACAGGTTCACGAGATGAGACTA 58.313 45.455 0.00 0.00 38.99 2.59
5515 9366 2.520069 ACAGGTTCACGAGATGAGACT 58.480 47.619 0.00 0.00 38.99 3.24
5516 9367 3.305398 AACAGGTTCACGAGATGAGAC 57.695 47.619 0.00 0.00 38.99 3.36
5570 9429 5.358298 AACTTTGTAAGAAATCAGGACGC 57.642 39.130 0.00 0.00 0.00 5.19
5571 9430 8.306680 TCTTAACTTTGTAAGAAATCAGGACG 57.693 34.615 0.00 0.00 37.20 4.79
5593 9452 6.746120 ACGTACACTGTACTTCTTGATTCTT 58.254 36.000 15.76 0.00 0.00 2.52
5596 9455 6.091437 GCTACGTACACTGTACTTCTTGATT 58.909 40.000 15.76 0.00 0.00 2.57
5614 9473 6.170506 TGGAATCTGAACTTATTTGCTACGT 58.829 36.000 0.00 0.00 0.00 3.57
5626 9485 1.745141 GCGATGGCTGGAATCTGAACT 60.745 52.381 0.00 0.00 35.83 3.01
5629 9488 0.252761 TTGCGATGGCTGGAATCTGA 59.747 50.000 0.15 0.00 40.82 3.27
5636 9495 0.099436 GCTTAGTTTGCGATGGCTGG 59.901 55.000 0.15 0.00 40.82 4.85
5692 9551 1.064952 CTTTGTGTTCGACGGGCTTTT 59.935 47.619 0.00 0.00 0.00 2.27
5823 9731 4.127171 GACTTTGACTGCTGACTAACCAA 58.873 43.478 0.00 0.00 0.00 3.67
5827 9735 4.345257 AGGAAGACTTTGACTGCTGACTAA 59.655 41.667 0.00 0.00 0.00 2.24
5861 9769 2.462503 GCGGATTGCGGTTGACTAA 58.537 52.632 0.00 0.00 0.00 2.24
5965 9879 3.717294 CTGCAGGGCCGGGTAACT 61.717 66.667 5.57 0.00 0.00 2.24
5990 9904 1.669115 CAGCGCTTGGTACACAGCT 60.669 57.895 7.50 4.76 41.81 4.24
5992 9906 3.566261 CCAGCGCTTGGTACACAG 58.434 61.111 7.50 0.00 42.41 3.66


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.